Cycles Bake yeilding bizarre textures and wrong colors- any ideas?
You've probably moved on by now, but for anyone with the same question, I had a similar issue just yesterday. I never quite figured out why exactly it was happening, but I eventually got the problem to go away by cleaning up my mesh. This included

adding and connecting some vertices to break up some large planes getting stretched at weird angles
dissolving unnecessary edges and vertices
deleting entire planes that were not going to be visible in the render
separating a part that I had awkwardly extruded and probably had some weird relationships with other vertices.